Todays python patches

Package-Manager: portage-2.2.17/cvs/Linux x86_64
Manifest-Sign-Key: 0xB9D4F231BD1558AB!

3 files changed, 188 insertions, 16 deletions

diff --git a/sci-chemistry/ccpn/ChangeLog b/sci-chemistry/ccpn/ChangeLog
index 9333e362dad2..0f8ef90ec58d 100644
--- a/sci-chemistry/ccpn/ChangeLog
+++ b/sci-chemistry/ccpn/ChangeLog
@@ -1,6 +1,11 @@
 # ChangeLog for sci-chemistry/ccpn
 # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccpn/ChangeLog,v 1.160 2015/02/23 11:42:36 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccpn/ChangeLog,v 1.161 2015/02/24 16:30:04 jlec Exp $
+
+*ccpn-2.4.1_p150224 (24 Feb 2015)
+
+  24 Feb 2015; Justin Lecher <jlec@gentoo.org> +ccpn-2.4.1_p150224.ebuild:
+  Todays python patches
 
 *ccpn-2.4.1_p150223 (23 Feb 2015)
 
diff --git a/sci-chemistry/ccpn/Manifest b/sci-chemistry/ccpn/Manifest
index e0af9ebe1b45..e4b6fd24d12d 100644
--- a/sci-chemistry/ccpn/Manifest
+++ b/sci-chemistry/ccpn/Manifest
@@ -17,29 +17,31 @@ DIST ccpn-update-2.4.1-150108.patch.xz 8364 SHA256 a2223d89dc279573871263093fedd
 DIST ccpn-update-2.4.1-150122.patch.xz 9032 SHA256 68c186762beb4600617f2dd71c14bacbc118311e0c9fc3c8ff53a22fc5caee05 SHA512 965ea204cee3ec54b7955c350769e497668fb2f134dbcc7c13d5169f49288e1855ed0824a9b4d8b39db990280145fe2e4f8de724eeddb2321db715e4a7565886 WHIRLPOOL f4c876a51cd4fb37f3dfd9a278f760c05bbf2a7f33c0e59d929d8c43ce931e4c6e177a05b084f9f7a57cc84895be071bf230c06c67fb7748d070e4f8db987b0d
 DIST ccpn-update-2.4.1-150202.patch.xz 9408 SHA256 75998daca8f25c212fcf50c122821949dda729102863e3c3c1cac66ce7bf02e3 SHA512 7d4e593d115e36a031178c13b0c1d237154091ee21ae0d35fae9246f2a0845f6ca2e81e7e0fab645355ac013fac3a0e46e9811916c55aa1c2239a640bc5c66f8 WHIRLPOOL 2b9134e31f137b823e10d3e93fc99bd217b6a5136f0c19c41e493eee58a30e5d4041699b6a13c858ac185f28ae9ccba25ff0ea935f577023b84ab00bfba90d66
 DIST ccpn-update-2.4.1-150223.patch.xz 10304 SHA256 3a045588005688466c13ca880de1ffb191ca8f8e277696d7420d6d19f375c9c5 SHA512 ac910a56f8221f1eefdc8d83b643aafb84a9e77169258e40c1e36b1bc95dba083f15488181d2ee34f22f341f989875825a77a318583537bd8fb4b0647a091421 WHIRLPOOL 05c02ba3ca614ec8dd586048a00c05fc66bf6fe2093f1bad2aa4ce69223fb498bc9640e72231765f86c5bb3f685e9b2c88dfe8a9afd9f43e130818ae62bb2aa8
+DIST ccpn-update-2.4.1-150224.patch.xz 10472 SHA256 8252e2e298b93c4cdf77cfb247d821a6ee3d95ee573fb03cd64e3c32a7bec9da SHA512 6905d352b8b12a6699de076e5bd8ce4c1efd561f4e062919550f8752ee1d9c304d57de18d13f810c71e12b236b70dc137d055efff6a2f2003c0bd42d4ca37540 WHIRLPOOL da5d69ee8ae9eca5536aa8a3cd5d01ba8c37cfb3b0cebbbd101d2bdeffef36399cb5454df51db62c4864051b1edb888bd8807c648564d736b0622adac699e8c4
 EBUILD ccpn-2.4.1.ebuild 4685 SHA256 6e4c496453063dee64e64975a5732f6bbbc820bb97dc460691187ad15dc3e935 SHA512 a862d7ea10818bf2f219411019db151255a1e09f8e72c7a37eacbe7220b8640958be43079e995828f055ae62e93d002540de5be8f0cff231bb5ec62dbb0e8a8e WHIRLPOOL 6ed8127f87305e1406aed474089a478423dc0ae6b3c81191d650de680d22aea2112c62ac63c02a76bf219bcad49451477682e3ad187999764bcb02fb105e1e58
 EBUILD ccpn-2.4.1_p150108.ebuild 4692 SHA256 cd8f2a9327714d07a88b714353299e078b6177444d746510e55dc7cb4c4b6e91 SHA512 94b835c77fec900191f3819934951938e864fa061e25c8a6e885af527947fd60510ec4dd8a65661996233d3de97fa0143803c7ba59508c79900676341e628721 WHIRLPOOL 638ec09624e702b0fc585a8eb63bf4070cd598e3b49032cfd4bd5f82219a77a16c832caec032f59b30e6ee1d4fbb41cbe7611a4d3b4e8c14f1f61a5942f79109
 EBUILD ccpn-2.4.1_p150122.ebuild 4692 SHA256 0c0b2c56576f3a3cc739daff25121339ba5f2f455e57ad76485246c30ba80399 SHA512 824858bba9edf362fee4154921230acba74362e2523a6fcb3807bcb61c37f3b21342433c8a9f4c2f2251f4ba3f472dae68da419f10fe018dedf61430cdd647b9 WHIRLPOOL abfa19b1bd70264997d8165dda26833c07a07b230c59c7e8305f209d4f5c20a78e4037ca89e12b3048f9ca7bde25b308d06e0e31db9d0ae3ed79bc4a1535bef0
 EBUILD ccpn-2.4.1_p150202.ebuild 4692 SHA256 d251bca04241d02f7235854d6756217e093370c7b5f11783fa1cc3c6e13d1593 SHA512 35a4f2b9c0825287b80997c338f3a393abbe9f6bb3eda067d530b02b58405ae1a0cb0bb9000f8667a5ee075e4b5fbbc56d6cc61406904d0102e513595c7525bc WHIRLPOOL 13f36b5c4954b530f0989969a27e2c662ecb08573fbccc7b6e2eb3f30f94b4badafde3049deab2e0166df8b5ffed24c705c54dc2a3fd1014718a217fb6505cba
 EBUILD ccpn-2.4.1_p150223.ebuild 4665 SHA256 9fdd0f3853099f79523ae3a02fb9b13cd00203fca252d2abfc81f078a2c48c71 SHA512 28d87e62296ef54ffc0e3f679295328810a59ed1263a078ef84969d0c8ffbde5bc99cd67dc576c4ee6b68d7b2a3c4387d8fe5de7bb1294638c008d451da09e20 WHIRLPOOL 4a7a66c93b5d0a91bbb59f9a0ae2ec028673b1c987822f41420cc570d804f2fb3285edd7a618415ff87013242414b101d9a6a140ab1f6841b0542503c772498c
-MISC ChangeLog 30259 SHA256 64d1b91079c91a568ff672c271dbe001fbfd1e49e96e8b7540bea788d5f6adfa SHA512 bbd6dedd6deef5e2002310bea2f3642960e96f87270c7cce19ae38f42bacc59e3b48275c1078ca88b4d6bc897426d10da07f9a0902cf0b09747594af797d308d WHIRLPOOL aee11016ef88247067d83d99d9fb797ae4a4117669f34c02ead730060ef70fa6f6c86884288604c8be0f9bb36759b859b99f8512674f15b6feb732ae148ccaa8
+EBUILD ccpn-2.4.1_p150224.ebuild 4665 SHA256 0584408fe4b5c066ab1187f418668c082e489f075e5b866523ae6e8f0a63ff32 SHA512 14b742ca202a61502baa92952dde26213bc4cbb77b70f51a57f2c6565244a4895a5b9a04188bbc6a83f27e8b6bf437232e3007badef3d1fd6b38902b84048f9b WHIRLPOOL 6003edd41c833dc196d39537e0d8ff6bd4457c37e13d97e52793527d9eed500a89ac40d78a7320fc4c6ec8ba82728b919842eb03965c4921ce6832bb38686e1d
+MISC ChangeLog 30394 SHA256 3ba149c39eec9d4607381b147f8d7c9f4e7eb747b144624c6b3783985c90665d SHA512 3a3492b701da5154cb047fa3491c222761b02071f4e6bd49a8fd334dc94fc99b397d404a0e8fcfe76597efbd4d69239ea1d890052c7d0fba53597824a9515b13 WHIRLPOOL 2a9b162891a302be7a565676ef74839937493a171b7b43e395b45dc76faa4fac99ad9db3eade2b2d944b3c9655280394abeb9f3aacaef958ec1dc92fadc36b83
 MISC metadata.xml 234 SHA256 8297e76ecd2cb828f604e9f138b263179eb84beb640215a0f60d7613eb46bb7f SHA512 0e94c0e6570a9267a39968d81c3b80680ccbc6eebb62199e4830b021a114c94a0de17ef2103cef62b7e27da1f51f225a30abb802aff82140ae6dc43366113d31 WHIRLPOOL fa6d4d90b092953b88ed3ad03e1e8c189296d268b39d13a4b4dcb78f0c4456341e3f1b44eea0860054fee43079179cb7cf7a912acf1fbe693ecdca6d9a65f081
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diff --git a/sci-chemistry/ccpn/ccpn-2.4.1_p150224.ebuild b/sci-chemistry/ccpn/ccpn-2.4.1_p150224.ebuild
new file mode 100644
index 000000000000..7ae01ae66bfa
--- /dev/null
+++ b/sci-chemistry/ccpn/ccpn-2.4.1_p150224.ebuild
@@ -0,0 +1,165 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ccpn/ccpn-2.4.1_p150224.ebuild,v 1.1 2015/02/24 16:30:04 jlec Exp $
+
+EAPI=5
+
+PYTHON_COMPAT=( python2_7 )
+PYTHON_REQ_USE="ssl,tk"
+
+inherit eutils flag-o-matic multilib portability python-single-r1 toolchain-funcs versionator
+
+PATCHSET="${PV##*_p}"
+MY_PN="${PN}mr"
+MY_PV="$(replace_version_separator 3 _ ${PV%%_p*})"
+MY_MAJOR="$(get_version_component_range 1-3)"
+
+DESCRIPTION="The Collaborative Computing Project for NMR"
+HOMEPAGE="http://www.ccpn.ac.uk/ccpn"
+SRC_URI="http://www-old.ccpn.ac.uk/download/${MY_PN}/analysis${MY_PV}.tar.gz"
+[[ -n ${PATCHSET} ]] \
+	&& SRC_URI+=" http://dev.gentoo.org/~jlec/distfiles/ccpn-update-${MY_MAJOR}-${PATCHSET}.patch.xz"
+
+SLOT="0"
+LICENSE="|| ( CCPN LGPL-2.1 )"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="+opengl"
+
+REQUIRED_USE="${PYTHON_REQUIRED_USE}"
+
+RDEPEND="
+	${PYTHON_DEPS}
+	dev-lang/tk[threads]
+	dev-python/numpy[${PYTHON_USEDEP}]
+	dev-tcltk/tix
+	=sci-libs/ccpn-data-"${MY_MAJOR}"*[${PYTHON_USEDEP}]
+	sci-biology/psipred
+	x11-libs/libXext
+	x11-libs/libX11
+	opengl? (
+		media-libs/freeglut
+		dev-python/pyglet[${PYTHON_USEDEP}] )"
+DEPEND="${RDEPEND}"
+
+RESTRICT="mirror"
+
+S="${WORKDIR}"/${MY_PN}/${MY_PN}$(get_version_component_range 1-2)
+
+src_prepare() {
+	[[ -n ${PATCHSET} ]] && \
+		EPATCH_OPTS="-p2" epatch "${WORKDIR}"/ccpn-update-${MY_MAJOR}-${PATCHSET}.patch
+
+	epatch "${FILESDIR}"/2.3.1-parallel.patch
+
+	append-lfs-flags
+
+	sed \
+		-e "/PSIPRED_DIR/s:'data':'share/psipred/data':g" \
+		-e "s:weights_s:weights:g" \
+		-i python/ccpnmr/analysis/wrappers/Psipred.py || die
+
+	local tk_ver
+	local myconf
+
+	tk_ver="$(best_version dev-lang/tk | cut -d- -f3 | cut -d. -f1,2)"
+
+	if use opengl; then
+		GLUT_NEED_INIT="-DNEED_GLUT_INIT"
+		IGNORE_GL_FLAG=""
+		GL_FLAG="-DUSE_GL_TRUE"
+		GL_DIR="${EPREFIX}/usr"
+		GL_LIB="-lglut -lGLU -lGL"
+		GL_INCLUDE_FLAGS="-I\$(GL_DIR)/include"
+		GL_LIB_FLAGS=""
+	else
+		IGNORE_GL_FLAG="-DIGNORE_GL"
+		GL_FLAG="-DUSE_GL_FALSE"
+	fi
+
+	GLUT_NOT_IN_GL=""
+	GLUT_FLAG="\$(GLUT_NEED_INIT) \$(GLUT_NOT_IN_GL)"
+
+	rm -rf data model doc license || die
+
+	sed \
+		-e "s|/usr|${EPREFIX}/usr|g" \
+		-e "s|^\(CC =\).*|\1 $(tc-getCC)|g" \
+		-e "s|^\(OPT_FLAG =\).*|\1 ${CPPFLAGS} ${CFLAGS}|g" \
+		-e "s|^\(LINK_FLAGS =.*\)|\1 ${LDFLAGS}|g" \
+		-e "s|^\(IGNORE_GL_FLAG =\).*|\1 ${IGNORE_GL_FLAG}|g" \
+		-e "s|^\(GL_FLAG =\).*|\1 ${GL_FLAG}|g" \
+		-e "s|^\(GL_DIR =\).*|\1 ${GL_DIR}|g" \
+		-e "s|^\(GL_LIB =\).*|\1 ${GL_LIB}|g" \
+		-e "s|^\(GL_LIB_FLAGS =\).*|\1 ${GL_LIB_FLAGS}|g" \
+		-e "s|^\(GL_INCLUDE_FLAGS =\).*|\1 ${GL_INCLUDE_FLAGS}|g" \
+		-e "s|^\(GLUT_NEED_INIT =\).*|\1 ${GLUT_NEED_INIT}|g" \
+		-e "s|^\(GLUT_NOT_IN_GL =\).*|\1|g" \
+		-e "s|^\(X11_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \
+		-e "s|^\(TCL_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \
+		-e "s|^\(TK_LIB =\).*|\1 -ltk|g" \
+		-e "s|^\(TK_LIB_FLAGS =\).*|\1 -L${EPREFIX}/usr/$(get_libdir)|g" \
+		-e "s|^\(PYTHON_INCLUDE_FLAGS =\).*|\1 -I$(python_get_includedir)|g" \
+		-e "s|^\(PYTHON_LIB =\).*|\1 -l${EPYTHON}|g" \
+		c/environment_default.txt > c/environment.txt || die
+
+	sed \
+		-e 's:ln -s:cp -f:g' \
+		-i $(find python -name linkSharedObjs) || die
+}
+
+src_compile() {
+	emake -C c all
+	emake -C c links
+}
+
+src_install() {
+	local libdir
+	local tkver
+	local _wrapper
+
+	find . -name "*.pyc" -type f -delete || die
+
+	libdir=$(get_libdir)
+	tkver=$(best_version dev-lang/tk | cut -d- -f3 | cut -d. -f1,2)
+
+	_wrapper="analysis dangle dataShifter depositionFileImporter eci formatConverter pipe2azara xeasy2azara extendNmr"
+	for wrapper in ${_wrapper}; do
+		sed \
+			-e "s|gentoo_sitedir|$(python_get_sitedir)|g" \
+		   -e "s|gentoolibdir|${EPREFIX}/usr/${libdir}|g" \
+			-e "s|gentootk|${EPREFIX}/usr/${libdir}/tk${tkver}|g" \
+			-e "s|gentootcl|${EPREFIX}/usr/${libdir}/tclk${tkver}|g" \
+			-e "s|gentoopython|${EPYTHON}|g" \
+			-e "s|gentoousr|${EPREFIX}/usr|g" \
+			-e "s|//|/|g" \
+			"${FILESDIR}"/${wrapper} > "${T}"/${wrapper} || die "Fail fix ${wrapper}"
+		dobin "${T}"/${wrapper}
+	done
+
+	local in_path=$(python_get_sitedir)/${PN}
+	local files
+	local pydocs
+
+	pydocs="$(find python -name doc -type d)"
+	rm -rf ${pydocs} || die
+
+	for i in python/memops/format/compatibility/{Converters,part2/Converters2}.py; do
+	sed \
+		-e 's|#from __future__|from __future__|g' \
+		-i ${i} || die
+	done
+
+	dodir ${in_path#${EPREFIX}}/c
+
+	ebegin "Installing main files"
+		python_moduleinto ${PN}
+		python_domodule python
+	eend
+
+	ebegin "Adjusting permissions"
+	for _file in $(find "${ED}" -type f -name "*so"); do
+		chmod 755 ${_file}
+	done
+	eend
+	python_optimize
+}